* Package: sci-chemistry/gromacs-2021.3-r1 * Repository: gentoo * Maintainer: alexxy@gentoo.org sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 custom-cflags doc double-precision elibc_musl fftw gmxapi gmxapi-legacy hwloc kernel_linux lmfit offensive openmp python_single_target_python3_9 single-precision threads tng userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox * Using python3.9 to build >>> Unpacking source... >>> Unpacking gromacs-2021.3.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work >>> Unpacking manual-2021.3.pdf to /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work unpack manual-2021.3.pdf: file format not recognized. Ignoring. >>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 ... * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3" * Build directory (BUILD_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_build" * Hardcoded definition(s) removed in CMakeLists.txt: * set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation * set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, op >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 ... * Configuring for float precision * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3" * Build directory (BUILD_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float" cmake -C /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_USE_LMFIT=EXTERNAL -DGMX_X11=no -DGMX_EXTERNAL_BLAS=no -DGMX_EXTERNAL_LAPACK=no -DGMX_OPENMP=yes -DGMX_COOL_QUOTES=yes -DGMX_USE_TNG=yes -DGMX_BUILD_MANUAL=no -DGMX_HWLOC=yes -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD=AVX2_256 -DGMX_VMD_PLUGIN_PATH=/usr/lib/vmd/plugins/*/molfile/ -DBUILD_TESTING=no -DGMX_BUILD_UNITTESTS=no -DPYTHON_EXECUTABLE=/usr/bin/python3.9 -DGMX_DOUBLE=OFF -DGMX_MPI=OFF -DGMX_THREAD_MPI=yes -DGMXAPI=yes -DGMX_INSTALL_LEGACY_API=yes -DGMX_GPU=OFF -DGMX_BINARY_SUFFIX= -DGMX_LIBS_SUFFIX= -DGMX_PYTHON_PACKAGE=no -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/gentoo_common_config.cmake -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-gentoo-linux-musl-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-gentoo-linux-musl-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/temp/python3.9/bin/python3 (found suitable version "3.9.9", minimum required is "3.6") found components: Interpreter -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - not found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - not found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - found -- Using manually set binary suffix: "" -- Using manually set library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Ryzen 9 5950X 16-Core Processor -- Detected build CPU family - 25 -- Detected build CPU model - 33 -- Detected build CPU stepping - 0 -- Detected build CPU features - aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Performing Test C_mavx2_mfma_FLAG_ACCEPTED -- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success -- Performing Test C_mavx2_mfma_COMPILE_WORKS -- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success -- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED -- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success -- Performing Test CXX_mavx2_mfma_COMPILE_WORKS -- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success -- Enabling 256-bit AVX2 SIMD instructions using CXX flags: -mavx2 -mfma -- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs -- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED -- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed -- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED -- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed -- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED -- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Success -- Performing Test C_mavx512f_mfma_COMPILE_WORKS -- Performing Test C_mavx512f_mfma_COMPILE_WORKS - Success -- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED -- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed -- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED -- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed -- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED -- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Success -- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS -- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS - Success -- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs - -mavx512f -mfma -- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED -- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "4.2.0", minimum required is "1.6.1") found components: pygments -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test LMFIT_LINKS_OK -- Performing Test LMFIT_LINKS_OK - Success CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (lmfit) does not match the name of the calling package (Lmfit). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/FindLmfit.cmake:84 (find_package_handle_standard_args) cmake/gmxManageLmfit.cmake:77 (find_package) src/gromacs/CMakeLists.txt:333 (gmx_manage_lmfit) This warning is for project developers. Use -Wno-dev to suppress it. -- Found lmfit: /usr/include/include (found version "9.0.0") -- <<< Gentoo configuration >>> Build type RelWithDebInfo Install path /usr Compiler flags: C -pipe -march=native -fno-diagnostics-color -O2 C++ -pipe -march=native -fno-diagnostics-color -O2 Linker flags: Executable -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Module -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float * Configuring for double precision * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3" * Build directory (BUILD_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_double" cmake -C /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_double/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_USE_LMFIT=EXTERNAL -DGMX_X11=no -DGMX_EXTERNAL_BLAS=no -DGMX_EXTERNAL_LAPACK=no -DGMX_OPENMP=yes -DGMX_COOL_QUOTES=yes -DGMX_USE_TNG=yes -DGMX_BUILD_MANUAL=no -DGMX_HWLOC=yes -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD=AVX2_256 -DGMX_VMD_PLUGIN_PATH=/usr/lib/vmd/plugins/*/molfile/ -DBUILD_TESTING=no -DGMX_BUILD_UNITTESTS=no -DPYTHON_EXECUTABLE=/usr/bin/python3.9 -DGMX_DOUBLE=ON -DGMX_MPI=OFF -DGMX_THREAD_MPI=yes -DGMXAPI=yes -DGMX_INSTALL_LEGACY_API=yes -DGMX_GPU=OFF -DGMX_BINARY_SUFFIX=_d -DGMX_LIBS_SUFFIX=_d -DGMX_PYTHON_PACKAGE=no -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_double/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_double/gentoo_common_config.cmake -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-gentoo-linux-musl-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-gentoo-linux-musl-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/temp/python3.9/bin/python3 (found suitable version "3.9.9", minimum required is "3.6") found components: Interpreter -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - not found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - not found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - found -- Using manually set binary suffix: "_d" -- Using manually set library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Ryzen 9 5950X 16-Core Processor -- Detected build CPU family - 25 -- Detected build CPU model - 33 -- Detected build CPU stepping - 0 -- Detected build CPU features - aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Performing Test C_mavx2_mfma_FLAG_ACCEPTED -- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success -- Performing Test C_mavx2_mfma_COMPILE_WORKS -- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success -- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED -- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success -- Performing Test CXX_mavx2_mfma_COMPILE_WORKS -- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success -- Enabling 256-bit AVX2 SIMD instructions using CXX flags: -mavx2 -mfma -- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs -- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED -- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed -- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED -- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed -- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED -- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Success -- Performing Test C_mavx512f_mfma_COMPILE_WORKS -- Performing Test C_mavx512f_mfma_COMPILE_WORKS - Success -- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED -- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed -- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED -- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed -- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED -- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Success -- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS -- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS - Success -- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs - -mavx512f -mfma -- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED -- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/libfftw3.so - found -- Using external FFT library - FFTW3 -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "4.2.0", minimum required is "1.6.1") found components: pygments -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test LMFIT_LINKS_OK -- Performing Test LMFIT_LINKS_OK - Success CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (lmfit) does not match the name of the calling package (Lmfit). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/FindLmfit.cmake:84 (find_package_handle_standard_args) cmake/gmxManageLmfit.cmake:77 (find_package) src/gromacs/CMakeLists.txt:333 (gmx_manage_lmfit) This warning is for project developers. Use -Wno-dev to suppress it. -- Found lmfit: /usr/include/include (found version "9.0.0") -- <<< Gentoo configuration >>> Build type RelWithDebInfo Install path /usr Compiler flags: C -pipe -march=native -fno-diagnostics-color -O2 C++ -pipe -march=native -fno-diagnostics-color -O2 Linker flags: Executable -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Module -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_double >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 ... * Compiling for float precision * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3" * Build directory (BUILD_DIR): 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/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/src/compression/xtc3.c [304/1119] cd /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3.9 -D HAVE_FULL_FUNCTIONING_PYTHON=Python3_Interpreter_FOUND -D PROJECT_VERSION=2021.3 -D PROJECT_SOURCE_DIR=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/VersionInfo.cmake -D VERSION_STRING_OF_FORK= -D SOURCE_IS_SOURCE_DISTRIBUTION=ON -P /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake [305/1119] /usr/bin/x86_64-gentoo-linux-musl-gcc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -Itng/include -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/external/zlib -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/src/lib/tng_io.c [306/1119] cd /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/src/gromacs && /usr/bin/cmake -D 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src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp FAILED: src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp In file included from /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp:47: /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h:172:5: error: 'int64_t' does not name a type 172 | int64_t numUpdates_; /**< The number of updates performed since the start of the simulation. */ | ^~~~~~~ /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h:60:1: note: 'int64_t' is defined in header ''; did you forget to '#include '? 59 | #include "gromacs/math/vectypes.h" +++ |+#include 60 | /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h: In member function 'int gmx::HistogramSize::numUpdates() const': /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h:146:37: error: 'numUpdates_' was not declared in this scope; did you mean 'numUpdates'? 146 | int numUpdates() const { return numUpdates_; } | ^~~~~~~~~~~ | numUpdates /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h: In member function 'void gmx::HistogramSize::incrementNumUpdates()': /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h:150:34: error: 'numUpdates_' was not declared in this scope; did you mean 'numUpdates'? 150 | void incrementNumUpdates() { numUpdates_ += 1; } | ^~~~~~~~~~~ | numUpdates /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp: In constructor 'gmx::HistogramSize::HistogramSize(const gmx::AwhBiasParams&, double)': /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp:68:5: error: class 'gmx::HistogramSize' does not have any field named 'numUpdates_' 68 | numUpdates_(0), | ^~~~~~~~~~~ /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'void gmx::HistogramSize::restoreFromHistory(const gmx::AwhBiasStateHistory&)': /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp:270:5: error: 'numUpdates_' was not declared in this scope; did you mean 'numUpdates'? 270 | numUpdates_ = stateHistory.numUpdates; | ^~~~~~~~~~~ | numUpdates /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'void gmx::HistogramSize::storeState(gmx::AwhBiasStateHistory*) const': /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp:281:46: error: 'numUpdates_' was not declared in this scope; did you mean 'numUpdates'? 281 | stateHistory->numUpdates = numUpdates_; | ^~~~~~~~~~~ | numUpdates [445/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/correlationtensor.cpp [446/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/pointstate.cpp [447/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/biasstate.cpp ninja: build stopped: subcommand failed. * ERROR: sci-chemistry/gromacs-2021.3-r1::gentoo failed (compile phase): * ninja -v -j4 -l0 failed * * Call stack: * ebuild.sh, line 127: Called src_compile * environment, line 3768: Called cmake_src_compile * environment, line 1466: Called cmake_build * environment, line 1435: Called eninja * environment, line 2376: Called die * The specific snippet of code: * "$@" || die "${nonfatal_args[@]}" "${*} failed" * * If you need support, post the output of `emerge --info '=sci-chemistry/gromacs-2021.3-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/gromacs-2021.3-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-chemistry:gromacs-2021.3-r1:20211209-224150.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float' * S: '/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3'